[ome-users] getPlane memory leak

[Alexander Tournier]

Hi Sebastien,

the exact error msg is:

Java exception occurred:
java.lang.OutOfMemoryError: Java heap space
     at IceInternal.BasicStream.readByteSeq(BasicStream.java:786)
     at Ice.ByteSeqHelper.read(ByteSeqHelper.java:26)
     at omero.api._RawPixelsStoreDelM.getPlane(_RawPixelsStoreDelM.java:523)
     at 
omero.api.RawPixelsStorePrxHelper.getPlane(RawPixelsStorePrxHelper.java:729)
     at 
omero.api.RawPixelsStorePrxHelper.getPlane(RawPixelsStorePrxHelper.java:701)

I've found a workaround,
I create the RawPixelsStore only once at the beginning of the program
and then reuse the same store throughout the analysis .. seems to work

Best,
Alex


On 01/05/13 11:25, Sebastien Besson wrote:
> Hi Alexander,
>
> I have not been able to reproduce your bug on our test servers using 
> the code you pasted below.
> Can you give us a little more information about:
> - the versions of the server and of OMERO.matlab you are using,
> - the size of the image you are working with,
> - how you know there is a Java memory leak. Do you get an exception 
> thrown in Matlab?
>
> Thanks
> Sebastien
>
> On 30 Apr 2013, at 18:55, Alexander Tournier wrote:
>
>> Hi there,
>>
>> I've been trolling the web for a solution to this but I just don't 
>> see it,
>> Any ideas why the following would create a memory leak in java??
>> Notice the close statement at the end!
>> And the offending object (IceInternal.Outgoing) is created during the 
>> call to setPixelsId according to visualvm and not destroyed by the 
>> close statement.
>>
>> store = session.createRawPixelsStore();
>> store.setPixelsId(imageId, false);
>>
>> Stack = zeros([sizeX,sizeY,sizeZ],'uint16');
>>
>> for z = 1:sizeZ
>>    plane = store.getPlane( z-1, channel, t);
>>    tPlane = toMatrix(plane, pixels);
>>    Stack(:,:,z) = tPlane;
>> end
>>
>> store.close();
>>
>>
>> Any ideas??
>> Thanks
>> Alexander
>>
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> Dr Sébastien Besson
> Open Microscopy Environment / Harvard Medical School
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
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We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. 
Cancer Research UK
Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103)
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Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
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